The organization and dynamics of the genome regulate DNA replication, DNA repair, and gene expression. Here, we developed a methodology for studies of 3D organization and dynamics of the nucleome over time scales ranging from milliseconds to hours, and length scales ranging from tens of nanometers to micrometers. We achieve unprecedented 3D track lengths throughout the mammalian nucleus by combining a novel labeling scheme using nanobody ArrayG/N fusions of dSpCas9 targeted to specific DNA loci; light sheet illumination for gentle imaging of live cells with high contrast; and point spread function engineering for parallel detection of multiple loci in 3D.
To obtain a complete picture of subcellular nanostructures, cells must be imaged with high resolution in all three dimensions (3D). Here, we present tilted light sheet microscopy with 3D point spread functions (TILT3D), an imaging platform that combines a novel, tilted light sheet illumination strategy with engineered long axial range point spread functions (PSFs) for low-background, 3D super localization of single molecules as well as 3D super-resolution imaging in thick cells. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The axial positions of the single molecules are encoded in the shape of the PSF rather than in the position or thickness of the light sheet, and the light sheet can therefore be formed using simple optics. The result is flexible and user-friendly 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validated TILT3D for 3D superresolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed Tetrapod PSF for fiducial bead tracking and live axial drift correction. We envision TILT3D to become an important tool not only for 3D super-resolution imaging, but also for live whole-cell single-particle and single-molecule tracking.
Point spread function (PSF) engineering has extended far-field localization microscopy into three dimensions by encoding the axial position of each emitter into the shape of its image on the detector. By fitting the observed PSF to a model function, one can extract position information with sub-diffraction precision. However, in practice this procedure is often complicated by optical aberrations present in the imaging system, which distort the shape of the observed PSF relative to the model function. The mismatch between the model and observed PSFs can limit the accuracy and precision achieved by the localization procedure.
Here, we present a simple method to experimentally improve the model PSF by phase retrieval of the pupil function of the imaging system using a set of images of an isolated emitter at different displacements from the focal plane. The pupil function is estimated by adding a phase term consisting of a combination of Zernike modes to the theoretical electric field at the back focal plane of the microscope. The amplitudes of the Zernike modes are determined by maximizing the likelihood function over all pixels in the experimental data set. Importantly, since all data is taken with the phase mask in place, we account for any aberrations it introduces. Using the resulting pupil function, we generate a model PSF which is significantly improved over the theoretical model in both the accuracy and precision of experimental emitter localizations. We also provide a MATLAB package which performs the entire fitting procedure, from phase retrieval to single-emitter localization.
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